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dna methylation
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0
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930
views
Estimate cell proportion from beta values using minfi estimateCellCounts?
minfi
cell proportion
estimateCellCounts
DNA Methylation
4.1 years ago
grayapply2009
• 0
1
vote
2
replies
1.8k
views
WGCNA on methylation data
normalization
DNA methylation
WGCNA
updated 4.9 years ago by
Peter Langfelder
★ 3.0k • written 4.9 years ago by
enora.fremy
• 0
1
vote
2
replies
966
views
Comparing more than 2 experimental groups with MEDIPS?
medips
medip-seq
dna methylation
dmr analysis
updated 5.4 years ago by
Lukas Chavez
▴ 570 • written 5.4 years ago by
mtefit
• 0
7
votes
7
replies
1.6k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R
gdc
rna-seq
dna methylation
updated 5.5 years ago by
Sean Davis
21k • written 5.5 years ago by
RichardJActon
▴ 50
1
vote
2
replies
1.1k
views
Odd Sample after SWAN normalisation, DNA methylation analysis EPIC array
minfi
normalization
outliers
dna methylation
densityplot
5.8 years ago
peter.fransquet
• 0
0
votes
0
replies
745
views
iEVORA wrapping up error
differential variability
dna methylation
iEVORA
DVP
6.0 years ago
poojitha.stemcell
▴ 10
0
votes
0
replies
1.0k
views
differential methylation analysis with RnBeads
rnbeads
methylation
methylationepic
dna methylation
6.2 years ago
gabrielrfries
• 0
0
votes
1
reply
1.1k
views
Problem in working with BiSeq - BSraw
dna methylation
biseq
updated 6.3 years ago by
Gordon Smyth
50k • written 6.3 years ago by
ahmad.moousavi
• 0
2
votes
5
replies
1.8k
views
Error when prepare the TCGAdata
tcgabiolinks
dna methylation
updated 6.4 years ago by
Marcel Ramos
690 • written 6.4 years ago by
michaelwxf2012
• 0
1
vote
1
reply
1.5k
views
Beta Value Analysis - DNA Methylation Dataset
dna methylation
illimina 450k methylation
beta
M
significance
updated 6.6 years ago by
James W. MacDonald
65k • written 6.6 years ago by
skids121
• 0
0
votes
0
replies
1.2k
views
DNA methylation 450k data - minfi - preprocessFunnorm - CNV cases vs non-CNV controls
CNV
minfi
preprocessing
dna methylation
7.1 years ago
Thomas
• 0
1
vote
2
replies
978
views
Correlating DNA methylation and Illumina gene expression microarray data
microarray
HM450
dna methylation
cohcap
updated 7.3 years ago by
James W. MacDonald
65k • written 7.3 years ago by
poojitha.stemcell
▴ 10
0
votes
1
reply
1.1k
views
error when using bumphunter package with illumina 450k data
minfi
bumphunter
DNA methylation
illumina450k
updated 7.9 years ago by
James W. MacDonald
65k • written 7.9 years ago by
fleur_p90
• 0
13 results • Page
1 of 1
Recent ...
Replies
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq
by
james.zhang20
• 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data
by
ATpoint
★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq
by
ATpoint
★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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